THE Australian Electoral Commission (AEC) wants part of the federal election declared void because it can't be certain who would have won the final two Senate places in WA.

In a petition lodged in the High Court today, AEC commissioner Ed Killesteyn said the loss of 1370 votes from WA means it is not possible to conclude which of the state's Senate candidates should go to Canberra.

"The court should be satisfied that the result of the election was likely to be affected and that it is just that the election (of WA senators) should be declared void,'' he said.

In the September 7 poll, WA voters had to select six senators, with Liberal David Johnston, Labor's Joe Bullock and Liberals Michaelia Cash and Linda Reynolds elected in the first four places.

In the initial count, the last two places went to Zhenya Wang of the Palmer United Party and Labor's Louise Pratt.

But because of the close result, Wayne Dropulich of the Australian Sports Party and the Greens Scott Ludlam requested a recount.

On the recount without the missing votes, Mr Dropulich and Senator Ludlam were elected.

But the AEC petition said that in a notional recount, without the missing votes but based on records, the final two places were decided by a single vote that would have sent Mr Wang and Ms Pratt to Canberra.

Mr Killesteyn said there were a number of contraventions of the Electoral Act by WA electoral officials including failing to properly conduct the recount and failing to maintain safe custody of ballot papers.

"If the 1370 missing ballot papers had been available for the recount, it was likely in the sense of there being a real chance, that the result of the election would have been different,'' he said.

The High Court can take the matter no further until the December 16 expiry of the 40-day time period from return of the election writs.

It's likely the case won't be heard until next year.

When the AEC realised the ballot papers were missing, it appointed former Australian Federal Police commissioner Mick Keelty to investigate.

His inquiry is continuing.

Special Minister of State Michael Ronaldson said the government had made its deep concerns clear to the AEC.

"The government expects the commission to conduct a detailed internal investigation as well as acting on any recommendations arising from the Keelty investigation,'' he said in a statement.